Tyrosine kinase inhibitors (TKI) are widely used to treat patients with leukemia driven by BCR-ABL11 and other oncogenic tyrosine kinases2,3. Recent efforts focused on the development of more potent TKI that also inhibit mutant tyrosine kinases4,5. However, even effective TKI typically fail to eradicate leukemia-initiating cells6–8, which often cause recurrence of leukemia after initially successful treatment. Here we report on the discovery of a novel mechanism of drug-resistance, which is based on protective feedback signaling of leukemia cells in response to TKI-treatment. We identified BCL6 as a central component of this drug-resistance pathway and demonstrate that targeted inhibition of BCL6 leads to eradication of drug-resistant and leukemia-initiating subclones. BCL6 is a known proto-oncogene that is often translocated in diffuse large B cell lymphoma (DLBCL)9. In response to TKI-treatment, BCR-ABL1 acute lymphoblastic leukemia (ALL) cells upregulate BCL6 protein levels by ~90-fold, i.e. to similar levels as in DLBCL (Fig. 1a). Upregulation of BCL6 in response to TKI-treatment represents a novel defense mechanism, which enables leukemia cells to survive TKI-treatment: Previous work suggested that TKI-mediated cell death is largely p53-independent. Here we demonstrate that BCL6 upregulation upon TKI-treatment leads to transcriptional inactivation of the p53 pathway. BCL6-deficient leukemia cells fail to inactivate p53 and are particularly sensitive to TKI-treatment. BCL6−/− leukemia cells are poised to undergo cellular senescence and fail to initiate leukemia in serial transplant recipients. A combination of TKI-treatment and a novel BCL6 peptide inhibitor markedly increased survival of NOD/SCID mice xenografted with patient-derived BCR-ABL1 ALL cells. We propose that dual targeting of oncogenic tyrosine kinases and BCL6-dependent feedback (Supplementary Fig. 1) represents a novel strategy to eradicate drug-resistant and leukemia-initiating subclones in tyrosine kinase-driven leukemia.

B-lymphoid transcription factors (e.g. PAX5, IKZF1) are critical for early B-cell development1–2, yet genetic lesions occur in >80% of cases of B-cell acute lymphoblastic leukemia (ALL)3–4. The significance of these lesions in ALL remained unclear. Combining ChIP-seq and RNA-seq studies, we identified a novel B-lymphoid program for transcriptional repression of glucose and energy supply. Our metabolic analyses revealed that PAX5 and IKZF1 enforce a state of chronic energy deprivation, resulting in constitutive activation of the energy-stress sensor AMPK5–7. Dominant-negative mutants of PAX5 and IKZF1 relieved glucose and energy restriction. Studying a transgenic pre-B ALL mouse model, heterozygous deletion of Pax5 increased glucose uptake and ATP-levels by >25-fold. Reconstitution of PAX5 and IKZF1 in pre-B ALL patient samples restored a non-permissive state and induced energy crisis and cell death. A CRISPR/Cas9-based screen of PAX5- and IKZF1- transcriptional targets identified NR3C1 (glucocorticoid receptor)8, TXNIP (glucose feedback sensor)9 and CNR2 (cannabinoid receptor)10 as central effectors of B-lymphoid restriction of glucose and energy supply. Interestingly, transport-independent lipophilic methyl-conjugates of pyruvate and TCA cycle metabolites bypassed the gatekeeper function of PAX5 and IKZF1 and readily enabled leukemic transformation. Conversely, pharmacological TXNIP- and CNR2-agonists and a small molecule AMPK-inhibitor strongly synergized with glucocorticoids, identifying TXNIP, CNR2 and AMPK as potential therapy-targets. Furthermore, our results provide a mechanistic explanation for the empiric finding that glucocorticoids are effective in the treatment of B-lymphoid but not myeloid malignancies. We conclude that B-lymphoid transcription factors function as metabolic gatekeepers by limiting the amount of cellular ATP to levels that are insufficient for malignant transformation.

SUMMARY Studying 830 pre-B ALL cases from four clinical trials, we found that human ALL can be divided into two fundamentally distinct subtypes based on pre-BCR function. While absent in the majority of ALL cases, tonic pre-BCR signaling was found in 112 cases (13.5%). In these cases, tonic pre-BCR signaling induced activation of BCL6, which in turn increased pre-BCR signaling output at the transcriptional level. Interestingly, inhibition of pre-BCR-related tyrosine kinases reduced constitutive BCL6 expression and selectively killed patient-derived pre-BCR+ ALL cells. These findings identify a genetically and phenotypically distinct subset of human ALL that critically depends on tonic pre-BCR signaling. In vivo treatment studies suggested that pre-BCR tyrosine kinase inhibitors are useful for the treatment of patients with pre-BCR+ ALL.

Robust SNP genotyping technologies and data analysis programs have encouraged researchers in recent years to use SNPs for linkage studies. Platforms used to date have been 10 K chip arrays, but the possible value of interrogating SNPs at higher densities has been considered. Here, we present a genome-wide linkage analysis by means of a 500 K SNP platform. The analysis was done on a large pedigree affected with Parkinsonian-pyramidal syndrome (PPS), and the results showed linkage to chromosome 22. Sequencing of candidate genes revealed a disease-associated homozygous variation (R378G) in FBXO7. FBXO7 codes for a member of the F-box family of proteins, all of which may have a role in the ubiquitin-proteosome protein-degradation pathway. This pathway has been implicated in various neurodegenerative diseases, and identification of FBXO7 as the causative gene of PPS is expected to shed new light on its role. The performance of the array was assessed and systematic analysis of effects of SNP density reduction was performed with the real experimental data. Our results suggest that linkage in our pedigree may have been missed had we used chips containing less than 100,000 SNPs across the genome.

B cells are selected for an intermediate level of B cell receptor (BCR) signaling strength: Attenuation below minimum (e.g. non-functional BCR)1 or hyperactivation above maximum (e.g. self-reactive BCR)2–3 thresholds of signaling strength causes negative selection. In ~25% of cases, acute lymphoblastic leukemia (ALL) cells carry the oncogenic BCR-ABL1 tyrosine kinase (Ph+), which mimics constitutively active pre-BCR signaling4,5. Current therapy approaches are largely focused on the development of more potent tyrosine kinase inhibitors to suppress oncogenic signaling below a minimum threshold for survival6. Here, we tested the hypothesis that targeted hyperactivation above a maximum threshold will engage a deletional checkpoint for removal of self-reactive B cells and selectively kill ALL cells. Testing various components of proximal pre-BCR signaling, we found that an incremental increase of Syk tyrosine kinase activity was required and sufficient to induce cell death. Hyperactive Syk was functionally equivalent to acute activation of a self-reactive BCR on ALL cells. Despite oncogenic transformation, this basic mechanism of negative selection was still functional in ALL cells. Unlike normal pre-B cells, patient-derived ALL cells express the inhibitory receptors PECAM1, CD300A and LAIR1 at high levels. Genetic studies revealed that Pecam1, Cd300a and Lair1 are critical to calibrate oncogenic signaling strength through recruitment of the inhibitory phosphatases Ptpn67 and Inpp5d8. Using a novel small molecule inhibitor of INPP5D9, we demonstrated that pharmacological hyperactivation of SYK and engagement of negative B cell selection represents a promising new strategy to overcome drug-resistance in human ALL.